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Statistical Applications in Genetics and Molecular Biology

2002 - 2012

from De Gruyter
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Volume 11, issue 5, 2012

DNA Pooling and Statistical Tests for the Detection of Single Nucleotide Polymorphisms pp. 1 Downloads
David M. Ramsey and Andreas Futschik
Comparison of Targeted Maximum Likelihood and Shrinkage Estimators of Parameters in Gene Networks pp. 2 Downloads
Geert Geeven, Mark J. van der Laan and Mathisca C.M. de Gunst
A PAUC-based Estimation Technique for Disease Classification and Biomarker Selection pp. 3 Downloads
Matthias Schmid, Torsten Hothorn, Friedemann Krause and Christina Rabe
Estimators of the local false discovery rate designed for small numbers of tests pp. 4 Downloads
Marta Padilla and David R. Bickel
Genotype Copy Number Variations using Gaussian Mixture Models: Theory and Algorithms pp. 5 Downloads
Chang-Yun Lin, Yungtai Lo and Kenny Q. Ye
Analyzing Genetic Association Studies with an Extended Propensity Score Approach pp. 6 Downloads
Huaqing Zhao, Timothy R. Rebbeck and Nandita Mitra
Empirical Bayesian Selection of Hypothesis Testing Procedures for Analysis of Sequence Count Expression Data pp. 7 Downloads
Stanley B. Pounds, Cuilan L. Gao and Hui Zhang
Detecting Differential Expression in RNA-sequence Data Using Quasi-likelihood with Shrunken Dispersion Estimates pp. 8 Downloads
Steven P. Lund, Dan Nettleton, Davis J. McCarthy and Gordon K. Smyth
Variational Bayes Procedure for Effective Classification of Tumor Type with Microarray Gene Expression Data pp. 9 Downloads
Takeshi Hayashi
Incorporating Genomic Annotation into a Hidden Markov Model for DNA Methylation Tiling Array Data pp. 10 Downloads
Gayla R. Olbricht, Bruce A. Craig and Rebecca W. Doerge
ExactDAS: An Exact Test Procedure for the Detection of Differential Alternative Splicing in Microarray Experiments pp. 11 Downloads
Tristan Mary-Huard, Florence Jaffrezic and Stéphane Robin
Large-scale Parentage Inference with SNPs: an Efficient Algorithm for Statistical Confidence of Parent Pair Allocations pp. 12 Downloads
Eric C. Anderson

Volume 11, issue 4, 2012

Computing Posterior Probabilities for Score-based Alignments Using ppALIGN pp. 1 Downloads
Stefan Wolfsheimer, Alexander Hartmann, Ralf Rabus and Gregory Nuel
QTL Mapping Using a Memetic Algorithm with Modifications of BIC as Fitness Function pp. 2 Downloads
Florian Frommlet, Ivana Ljubic, Helga Björk Arnardóttir and Malgorzata Bogdan
A Bayesian autoregressive three-state hidden Markov model for identifying switching monotonic regimes in Microarray time course data pp. 3 Downloads
Alessio Farcomeni and Serena Arima
Performance of MAX Test and Degree of Dominance Index in Predicting the Mode of Inheritance pp. 4 Downloads
Elias Zintzaras and Mauro Santos
A Novel and Fast Normalization Method for High-Density Arrays pp. 5 Downloads
Maarten van Iterson, Floor A.M. Duijkers, Jules P.P. Meijerink, Pieter Admiraal, Gert-Jan B. van Ommen, Judith M. Boer, Max M. van Noesel and Renee X. Menezes
An Integrated Hierarchical Bayesian Model for Multivariate eQTL Mapping pp. 6 Downloads
Marie Pier Scott-Boyer, Gregory C. Imholte, Arafat Tayeb, Aurelie Labbe, Christian F. Deschepper and Raphael Gottardo
A Non-Homogeneous Dynamic Bayesian Network with Sequentially Coupled Interaction Parameters for Applications in Systems and Synthetic Biology pp. 7 Downloads
Marco Grzegorczyk and Dirk Husmeier
Correction for Founder Effects in Host-Viral Association Studies via Principal Components pp. 8 Downloads
Karyn L. Reeves, Elizabeth J. McKinnon and Ian R. James
Testing clonality of three and more tumors using their loss of heterozygosity profiles pp. 9 Downloads
Irina Ostrovnaya
Estimating the Number of One-step Beneficial Mutations pp. 10 Downloads
Andrzej J. Wojtowicz, Craig R. Miller and Paul Joyce
Incorporating the Empirical Null Hypothesis into the Benjamini-Hochberg Procedure pp. 11 Downloads
Debashis Ghosh
How to analyze many contingency tables simultaneously in genetic association studies pp. 12 Downloads
Thorsten Dickhaus, Klaus Straßburger, Daniel Schunk, Carlos Morcillo-Suarez, Thomas Illig and Arcadi Navarro
Cluster-Localized Sparse Logistic Regression for SNP Data pp. 13 Downloads
Harald Binder, Tina Müller, Holger Schwender, Klaus Golka, Michael Steffens, Jan G. Hengstler, Katja Ickstadt and Martin Schumacher
Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications pp. 14 Downloads
Toby Kenney and Hong Gu
A New Explained-Variance Based Genetic Risk Score for Predictive Modeling of Disease Risk pp. 15 Downloads
Ronglin Che and Alison A. Motsinger-Reif

Volume 11, issue 3, 2012

A New Approach for the Joint Analysis of Multiple Chip-Seq Libraries with Application to Histone Modification pp. 1 Downloads
John P. Ferguson, Judy H. Cho and Hongyu Zhao
Sample Size Calculations for Designing Clinical Proteomic Profiling Studies Using Mass Spectrometry pp. 2 Downloads
Stephen O. Nyangoma, Stuart I. Collins, Douglas G. Altman, Philip Johnson and Lucinda J. Billingham
Graph Selection with GGMselect pp. 3 Downloads
Christophe Giraud, Sylvie Huet and Nicolas Verzelen
Non-Iterative, Regression-Based Estimation of Haplotype Associations with Censored Survival Outcomes pp. 4 Downloads
Benjamin French, Thomas Lumley, Thomas P. Cappola and Nandita Mitra
Detection of Differentially Expressed Gene Sets in a Partially Paired Microarray Data Set pp. 5 Downloads
Johan Lim, Jayoun Kim, Sang-cheol Kim, Donghyeon Yu, Kyunga Kim and Byung Soo Kim
GENOVA: Gene Overlap Analysis of GWAS Results pp. 6 Downloads
Clara S. Tang and Manuel A. R. Ferreira
Empirical Bayes Interval Estimates that are Conditionally Equal to Unadjusted Confidence Intervals or to Default Prior Credibility Intervals pp. 7 Downloads
David R. Bickel
Combining Multiple Laser Scans of Spotted Microarrays by Means of a Two-Way ANOVA Model pp. 8 Downloads
Jérôme Ambroise, Bertrand Bearzatto, Annie Robert, Benoit Macq and Jean-Luc Gala
Normalization, bias correction, and peak calling for ChIP-seq pp. 9 Downloads
Aaron Diaz, Kiyoub Park, Daniel A. Lim and Jun S. Song
The practical effect of batch on genomic prediction pp. 10 Downloads
Hilary S. Parker and Jeffrey T. Leek
Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies pp. 11 Downloads
Jasmina Bogojeska and Thomas Lengauer
Borrowing Information Across Genes and Experiments for Improved Error Variance Estimation in Microarray Data Analysis pp. 12 Downloads
Tieming Ji, Peng Liu and Dan Nettleton
Detecting Sample Misidentifications in Genetic Association Studies pp. 13 Downloads
Claus T. Ekstrøm and Bjarke Feenstra
The Beta-Binomial SGoF method for multiple dependent tests pp. 14 Downloads
Jacobo de Uña-Alvarez
Exploring Multicollinearity Using a Random Matrix Theory Approach pp. 15 Downloads
Kristen Feher, James Whelan and Samuel Müller

Volume 11, issue 2, 2012

Special Issue on Computational Statistical Methods for Genomics and Systems Biology pp. 1 Downloads
Aurélie Labbe and Sandrine Dudoit
A Generalized Hidden Markov Model for Determining Sequence-based Predictors of Nucleosome Positioning pp. 2 Downloads
Carlee Moser and Mayetri Gupta
Gene Filtering in the Analysis of Illumina Microarray Experiments pp. 3 Downloads
Anyiawung Chiara Forcheh, Geert Verbeke, Adetayo Kasim, Dan Lin, Ziv Shkedy, Willem Talloen, Hinrich WH Göhlmann and Lieven Clement
Principal Components of Heritability for High Dimension Quantitative Traits and General Pedigrees pp. 4 Downloads
Karim Oualkacha, Aurelie Labbe, Antonio Ciampi, Marc-Andre Roy and Michel Maziade
Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors pp. 5 Downloads
Anthony Lee, Francois Caron, Arnaud Doucet and Chris Holmes
A Family-Based Probabilistic Method for Capturing De Novo Mutations from High-Throughput Short-Read Sequencing Data pp. 6 Downloads
Reed A. Cartwright, Julie Hussin, Jonathan E. M. Keebler, Eric A. Stone and Philip Awadalla
Adjusting for Spurious Gene-by-Environment Interaction Using Case-Parent Triads pp. 7 Downloads
Ji-Hyung Shin, Claire Infante-Rivard, Jinko Graham and Brad McNeney
Querying Genomic Databases: Refining the Connectivity Map pp. 8 Downloads
Mark R. Segal, Hao Xiong, Henrik Bengtsson, Richard Bourgon and Robert Gentleman
A Model-Based Analysis to Infer the Functional Content of a Gene List pp. 9 Downloads
Michael A. Newton, Qiuling He and Christina Kendziorski
Candidate Pathway Based Analysis for Cleft Lip with or without Cleft Palate pp. 10 Downloads
Tian-Xiao Zhang, Terri H. Beaty and Ingo Ruczinski
Improving Pedigree-based Linkage Analysis by Estimating Coancestry Among Families pp. 11 Downloads
Chris Glazner and Elizabeth Alison Thompson

Volume 11, issue 1, 2012

Improving Hidden Markov Models for Classification of Human Immunodeficiency Virus-1 Subtypes through Linear Classifier Learning pp. 1 Downloads
Ingo Bulla, Anne-Kathrin Schultz and Peter Meinicke
Transcriptional Network Inference from Functional Similarity and Expression Data: A Global Supervised Approach pp. 2 Downloads
Jérôme Ambroise, Annie Robert, Benoit Macq and Jean-Luc Gala
Alignment-free Sequence Comparison for Biologically Realistic Sequences of Moderate Length pp. 3 Downloads
Conrad J. Burden, Junmei Jing and Susan R. Wilson
Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays pp. 4 Downloads
Lieven Clement, Kristof De Beuf, Olivier Thas, Marnik Vuylsteke, Rafael A. Irizarry and Ciprian M. Crainiceanu
A Context Dependent Pair Hidden Markov Model for Statistical Alignment pp. 5 Downloads
Ana Arribas-Gil and Catherine Matias
MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection pp. 6 Downloads
Malay Bhattacharyya, Lars Feuerbach, Tapas Bhadra, Thomas Lengauer and Sanghamitra Bandyopadhyay
Fast Identification of Biological Pathways Associated with a Quantitative Trait Using Group Lasso with Overlaps pp. 7 Downloads
Matt Silver, Giovanni Montana and Alzheimer's Disease Neuroimaging Initiative
A Mixture-Model Approach for Parallel Testing for Unequal Variances pp. 8 Downloads
Haim Y. Bar, James G. Booth and Martin T. Wells
Stopping-Time Resampling and Population Genetic Inference under Coalescent Models pp. 9 Downloads
Paul A. Jenkins
Optimality Criteria for the Design of 2-Color Microarray Studies pp. 10 Downloads
Kathleen F. Kerr
The Inheritance Procedure: Multiple Testing of Tree-structured Hypotheses pp. 11 Downloads
Jelle J. Goeman and Livio Finos
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